rs3755325

Positions:

• chr2-241234501-G-A
• chr2-241234501-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005336.6(HDLBP):​c.3145-538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,000 control chromosomes in the GnomAD database, including 14,606 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (14606 hom., cov: 32)
• Consequence: HDLBP NM_005336.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

Genes affected

HDLBP (HGNC:4857): (high density lipoprotein binding protein) The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

ANO7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HDLBP	NM_005336.6	c.3145-538C>T		intron_variant		ENST00000310931.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HDLBP	ENST00000310931.10	c.3145-538C>T		intron_variant		1	NM_005336.6	P1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64008 AN: 151882 Hom.: 14603 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.465

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.421 AC: 64029 AN: 152000 Hom.: 14606 Cov.: 32 AF XY: 0.415 AC XY: 30837 AN XY: 74304

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.460

Alfa AF: 0.496 Hom.: 21432

Bravo AF: 0.420

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3755325; hg19: chr2-242173916;